[Immune reconstitution and influencing factors in HIV infected men who have sex with men with access to antiviral therapy in Guangxi Zhuang Autonomous Region from 2005 to 2021]

Objective: To analyze immune reconstitution and influencing factors in HIV infected men who have sex with men (MSM) with access to antiviral therapy (ART) in Guangxi Zhuang Autonomous Region (Guangxi) during 2005-2021. Methods: The data were collected from Chinese Disease Prevention and Control Information System. The study subjects were HIV infected MSM with access to the initial ART for ≥24 weeks in Guangxi from 2005 to 2021 and HIV RNA lower than the detection limit within 24 months. The proportion of infected MSM who had immune reconstitution after ART was calculated. Cox proportional hazard regression model was used to analyze the influencing factors of immune reconstitution. Software SPSS 24.0 was used for statistical analysis. Results: A total of 3 200 HIV infected MSM were enrolled, in whom 15.56 % (498/3 200) had no immune reconstitution, 14.78% (473/3 200) had moderate immune reconstitution, and the rate of complete immune reconstitution was 69.66% (2 229/3 200). The M (Q1, Q3) of ART time for immune reconstitution was 12 (5, 27) months. Multivariate Cox proportional risk regression model analysis results showed that compared with those with initial ART at age ≥30 years, WHO clinical stage Ⅲ/Ⅳ illness, baseline BMI <18.50 kg/m2 and baseline CD4+T lymphocyte (CD4) counts <200 cells/µl, HIV infected MSM with initial ART at age <30 years, WHO clinical stageⅠ/Ⅱ illness, baseline BMI≥24.00 kg/m2 and baseline CD4 counts ≥200 cells/µl were more likely to have complete immune reconstitution. Conclusions: In the HIV infected MSM in Guangxi, failures to achieve moderate and complete immune reconstitution were observed. Surveillance and ART regimen should be improved for key populations, such as those with older age and low baseline CD4 counts.

[Fabrication and evaluation of composite hydroxyapatite coating on ordered micro-/nanotextured titanium surface]

Objective: To develope a titanium specimen with good osteogenic activity through fabrication of a composite hydroxyapatite coating on ordered micro-/nanotextured titanium surface. Methods: An ordered micro-/nanotextured structure was prepared on the surface of titanium (the control), and then hydroxyapatite was deposited on the as-prepared ordered micro-/nanotextured structure by alternative loop immersion method. The ordered micro-/nanotextured structures before and after hydroxyapatite deposition were denoted as HA and MN, respectively. Surface morphology was observed using a scanning electron microscope. Bone marrow mesenchymal stem cells (BMMSC) were seeded on the surface of three different materials. Cell morphology was observed with a scanning electron microscope. Cell adhesion and cell proliferation were evaluated using 4', 6-diamidino-2-phenylindole staining and cell counting kit-8 assay, respectively. Extracellular matrix mineralization and the expression levels of osteogenesis-related genes were evaluated by alizarin red staining and real-time quantitative PCR, respectively. Each group has three samples in every experiment. Results: After alternative loop immersing, the MN's original microholes (20 μm in diameter) were retained, and the uniform petal-like hydroxyapatite was deposited on the MN's original titania nanotubes (70 nm in diameter). Compared with the control, BMMSC on MN and HA elongated further and intersected along the micron structure with noticeable pseudopodia and pseudoplates, and the trend was more pronounced especially on HA. The number of early adherent cells on HA was remarkably larger than that on the control and MN at each time point (P<0.05). On day 1, the A value of cell proliferation on HA was significantly higher than that on the control and MN (P<0.05). The A value of cell proliferation on HA was significantly lower than that on the control and MN on day 3 (P<0.05). On day 7, the A value of cell proliferation on HA was significantly lower than that on MN (P<0.05), but there was no statistically significant difference in the A value of cell proliferation between HA and the control on day 7 (P>0.05). The Avalue of extracellular matrix mineralization on HA (0.607±0.011) was significantly higher than that on the control and MN (0.268±0.025 and 0.522±0.022, respectively) (t=-0.25, P<0.001; t=-0.34, P<0.001). The expression levels of bone related genes on HA were significantly higher than those on the control and MN (P<0.05). Conclusions: HA could promote the BMMSC adhesion and osteogenic differentiation, support BMMSC proliferation, and demonstrate good osteogenic activity.

[A multicenter study to test the reliability and validity of the frailty assessment scale for elderly patients with inguinal hernia and to evaluate the value of clinical application]

Objectives: To verify the reliability and validity of the frailty assessment scale for elderly patients with inguinal hernia and to evaluate the value of its clinical application. Methods: A convenience sampling method was used to collect 129 geriatric patients who underwent inguinal hernia surgery from January 2018 to January 2023 in nine hospitals in Liaoning Province. There were 120 males and 9 females, of whom 89 patients were 60 to <75 years old, 33 patients were 75 to <85 years old and 7 patients were ≥85 years old. The 129 patients included 11 elderly patients with inguinal hernia who had recovered from preoperative infection with COVID-19. Statistical methods such as Cronbach's coefficient, Kaiser-Meyer-Olkin test, Bartlett's test, Pearson's correlation analysis, etc. were calculated to verify the reliability indexes such as feasibility, content validity, structural validity, criterion-related validity, internal consistency reliability, and re-test reliability. Taking the 5-item modified frailty index (5-mFI) as the gold standard, the area under the curve was used to analyze the ability of the two scales to predict the occurrence of postoperative acute urinary retention, postoperative delirium, poor incision healing, operative hematoma seroma, and postoperative complications. Results: The frailty assessment scale for elderly patients with inguinal hernia showed good reliability and validity (valid completion rate of 99.2%; item content validity index of 1.000, and the scale content validity index of 1.000; exploratory factor analysis extracted a total of 1 principal component, and factor loadings of each item of 0.565 to 0.873; the AUC for frailty diagnosis using 5-mFI as the gold standard of 0.795 (P<0.01) Cronbach's coefficient of 0.916, retest reliability coefficient of 0.926), it could effectively predict postoperative acute urinary retention, delirium, hematoma seroma in the operative area and total complications (AUC of 0.746, 0.870, 0.806, and 0.738, respectively; all P<0.05), and prediction efficiency was higher than that of 5-mFI (AUC of 0.694, 0.838, 0.626 and 0.641, P<0.05 for delirium only), but both scales were inaccurate in predicting poor incision healing (AUC of 0.519, P=0.913 for the frailty assessment scale and 0.455, P=0.791 for the 5-mFI). Conclusions: The frailty assessment scale for elderly patients with inguinal hernia is reliable and significantly predicts the occurrence of postoperative adverse events in elderly inguinal hernia patients. The scale can also be used for preoperative frailty assessment in elderly patients with inguinal hernia after rehabilitation from COVID-19 infection.

Translating GWAS Findings to Inform Drug Repositioning Strategies for COVID-19 Treatment

We developed a computational framework that integrates Genome-Wide Association Studies (GWAS) and post-GWAS analyses, designed to facilitate drug repurposing for COVID-19 treatment. The comprehensive approach combines transcriptomic-wide associations, polygenic priority scoring, 3D genomics, viral-host protein-protein interactions, and small-molecule docking. Through GWAS, we identified nine druggable host genes associated with COVID-19 severity and SARS-CoV-2 infection, all of which show differential expression in COVID-19 patients. These genes include IFNAR1, IFNAR2, TYK2, IL10RB, CXCR6, CCR9, and OAS1. We performed an extensive molecular docking analysis of these targets using 553 small molecules derived from five therapeutically enriched categories, namely antibacterials, antivirals, antineoplastics, immunosuppressants, and anti-inflammatories. This analysis, which comprised over 20,000 individual docking analyses, enabled the identification of several promising drug candidates. All results are available via the DockCoV2 database (https://dockcov2.org/drugs/). The computational framework ultimately identified nine potential drug candidates: Peginterferon alfa-2b, Interferon alfa-2b, Interferon beta-1b, Ruxolitinib, Dactinomycin, Rolitetracycline, Irinotecan, Vinblastine, and Oritavancin. While its current focus is on COVID-19, our proposed computational framework can be applied more broadly to assist in drug repurposing efforts for a variety of diseases. Overall, this study underscores the potential of human genetic studies and the utility of a computational framework for drug repurposing in the context of COVID-19 treatment, providing a valuable resource for researchers in this field.

[Analysis of late-diagnosis and associated factors in newly reported HIV infections among men who have sex with men in Guangxi Zhuang Autonomous Region, 2005-2021]

Objective: To analyze the trend of late-diagnosis of HIV-infected men who have sex with men (MSM) before and after the AIDS Conquering Project in Guangxi Zhuang Autonomous Region (Guangxi) and its influencing factors, in order to find out the population groups that need priority intervention at the present stage. Methods: The HIV-infected MSM in Guangxi from 2005-2021 were selected from the National Integrated HIV/AIDS Control and Prevention Data System. The Joinpoint 4.9.1.0 software was used to test the time trend of late-diagnosis and non-late-diagnosis cases, and logistic regression was applied to analyze the factors influencing the proportion of late-diagnosis at each stage. Results: From 2005 to 2021, 5 764 HIV-infected MSM were reported in Guangxi from 2005 to 2021, with an overall late-diagnosis of 28.45% (1 640 cases). Under the 2015 baseline data as the boundary, the proportion of late-diagnosis cases showed a trend of sharp decline followed by stabilization from 2005 to 2015, average annual percent change= -6.90% (P<0.001). The effect of factors such as resident population, occupation as a farmer or worker, and sample originating from medical consultation on late-diagnosis changed considerably before and after the implementation of the project, and the factors influencing late-diagnosis at this stage were age, resident population, occupation as a farmer, worker or student. The factors influencing late-diagnosis at this stage are age, resident population, and occupation as a farmer, worker and a student. Conclusions: The proportion of late diagnosis cases of HIV-infected MSM in Guangxi decreased significantly before and after the project. However, late-diagnosis should not be neglected and precise prevention and control should be carried out for the resident population, farmers, workers or students.

TRIPBASE: a database for identifying the human genomic DNA and lncRNA triplexes

Long-non-coding RNAs (lncRNAs) are defined as RNA sequences which are >200 nt with no coding capacity. These lncRNAs participate in various biological mechanisms, and are widely abundant in a diversity of species. There is well-documented evidence that lncRNAs can interact with genomic DNAs by forming triple helices (triplexes). Previously, several computational methods have been designed based on the Hoogsteen base-pair rule to find theoretical RNA-DNA:DNA triplexes. While powerful, these methods suffer from a high false-positive rate between the predicted triplexes and the biological experiments. To address this issue, we first collected the experimental data of genomic RNA-DNA triplexes from antisense oligonucleotide (ASO)-mediated capture assays and used Triplexator, the most widely used tool for lncRNA-DNA interaction, to reveal the intrinsic information on true triplex binding potential. Based on the analysis, we proposed six computational attributes as filters to improve the in-silico triplex prediction by removing most false positives. Further, we have built a new database, TRIPBASE, as the first comprehensive collection of genome-wide triplex predictions of human lncRNAs. In TRIPBASE, the user interface allows scientists to apply customized filtering criteria to access the potential triplexes of human lncRNAs in the cis-regulatory regions of the human genome. TRIPBASE can be accessed at https://tripbase.iis.sinica.edu.tw/.

Improved Measurement of the Evolution of the Reactor Antineutrino Flux and Spectrum at Daya Bay

Reactor neutrino experiments play a crucial role in advancing our knowledge of neutrinos. In this Letter, the evolution of the flux and spectrum as a function of the reactor isotopic content is reported in terms of the inverse-beta-decay yield at Daya Bay with 1958 days of data and improved systematic uncertainties. These measurements are compared with two signature model predictions: the Huber-Mueller model based on the conversion method and the SM2018 model based on the summation method. The measured average flux and spectrum, as well as the flux evolution with the ^{239}Pu isotopic fraction, are inconsistent with the predictions of the Huber-Mueller model. In contrast, the SM2018 model is shown to agree with the average flux and its evolution but fails to describe the energy spectrum. Altering the predicted inverse-beta-decay spectrum from ^{239}Pu fission does not improve the agreement with the measurement for either model. The models can be brought into better agreement with the measurements if either the predicted spectrum due to ^{235}U fission is changed or the predicted ^{235}U, ^{238}U, ^{239}Pu, and ^{241}Pu spectra are changed in equal measure.

Precision Measurement of Reactor Antineutrino Oscillation at Kilometer-Scale Baselines by Daya Bay

We present a new determination of the smallest neutrino mixing angle θ_{13} and the mass-squared difference Δm_{32}^{2} using a final sample of 5.55×10^{6} inverse beta-decay (IBD) candidates with the final-state neutron captured on gadolinium. This sample is selected from the complete dataset obtained by the Daya Bay reactor neutrino experiment in 3158 days of operation. Compared to the previous Daya Bay results, selection of IBD candidates has been optimized, energy calibration refined, and treatment of backgrounds further improved. The resulting oscillation parameters are sin^{2}2θ_{13}=0.0851±0.0024, Δm_{32}^{2}=(2.466±0.060)×10^{-3}  eV^{2} for the normal mass ordering or Δm_{32}^{2}=-(2.571±0.060)×10^{-3}  eV^{2} for the inverted mass ordering.

Pediatric Cardiology Fellowship Standards for Training in Exercise Medicine and Curriculum Outline

Over the past 2 decades, fundamentals of exercise medicine, including clinical exercise testing, assessment and promotion of physical activity, exercise prescription, and supervised exercise training/rehabilitation programming have demonstrated considerable clinical value in the management of children and adolescents with congenital and acquired heart disease. Although the principles of exercise medicine have become an integral component in pediatric cardiology, there are no standardized training recommendations for exercise physiology during pediatric cardiology fellowship at this time. Thus, the Pediatric Cardiology Exercise Medicine Curriculum Committee (PCEMCC) was formed to establish core and advanced exercise physiology training recommendations for pediatric cardiology trainees. The PCEMCC includes a diverse group of pediatric cardiologists, exercise physiologists, and fellowship program directors. The expert consensus training recommendations are by no means a mandate and are summarized herein, including suggestions for achieving the minimum knowledge and training needed for general pediatric cardiology practice.

Genome-wide analyses identify novel risk loci for cluster headache in Han Chinese residing in Taiwan

BACKGROUND

Cluster headache is a highly debilitating neurological disorder with considerable inter-ethnic differences. Genome-wide association studies (GWAS) recently identified replicable genomic loci for cluster headache in Europeans, but the genetic underpinnings for cluster headache in Asians remain unclear. The objective of this study is to investigate the genetic architecture and susceptibility loci of cluster headache in Han Chinese resided in Taiwan.

METHODS

We conducted a two-stage genome-wide association study in a Taiwanese cohort enrolled from 2007 through 2022 to identify the genetic variants associated with cluster headache. Diagnosis of cluster headache was retrospectively ascertained with the criteria of International Classification of Headache Disorders, third edition. Control subjects were enrolled from the Taiwan Biobank. Genotyping was conducted with the Axiom Genome-Wide Array TWB chip, followed by whole genome imputation. A polygenic risk score was developed to differentiate patients from controls. Downstream analyses including gene-set and tissue enrichment, linkage disequilibrium score regression, and pathway analyses were performed.

RESULTS

We enrolled 734 patients with cluster headache and 9,846 population-based controls. We identified three replicable loci, with the lead SNPs being rs1556780 in CAPN2 (odds ratio = 1.59, 95% CI 1.42‒1.78, p = 7.61 × 10^-16), rs10188640 in MERTK (odds ratio = 1.52, 95% CI 1.33‒1.73, p = 8.58 × 10^-13), and rs13028839 in STAB2 (odds ratio = 0.63, 95% CI 0.52‒0.78, p = 2.81 × 10^-8), with the latter two replicating the findings in European populations. Several previously reported genes also showed significant associations with cluster headache in our samples. Polygenic risk score differentiated patients from controls with an area under the receiver operating characteristic curve of 0.77. Downstream analyses implicated circadian regulation and immunological processes in the pathogenesis of cluster headache.

CONCLUSIONS

This study revealed the genetic architecture and novel susceptible loci of cluster headache in Han Chinese residing in Taiwan. Our findings support the common genetic contributions of cluster headache across ethnicities and provide novel mechanistic insights into the pathogenesis of cluster headache.

[Factors associated with death and attrition in HIV-infected children under initial antiretroviral therapy in Guangxi Zhuang Autonomous Region, 2004 - 2019]

Objective: To investigate death and attrition in HIV-infected children under initial antiretroviral therapy (ART) and associated factors in Guangxi Zhuang autonomous region. Methods: This retrospective cohort study was conducted in HIV-infected children under initial ART in Guangxi from 2004 to 2019, data from ART information system of National comprehensive AIDS prevention and treatment information system. Cox proportional hazards models were used to assess factors associated with the death and attrition. Results: In 943 HIV-infected children, the overall mortality and attrition rates were 1.00/100 person-years and 0.77/100 person-years, respectively. The mortality and attrition rates within the first year of ART were 3.90/100 person-years and 1.67/100 person-years, respectively. The cumulative survival rate during the first, second, fifth and tenth year after ART was 96.14%, 95.80%, 93.68% and 91.54%, respectively. Multivariate Cox proportional hazards models results showed that being female (aHR=2.00, 95%CI: 1.17-3.40), CD4⁺T lymphocytes (CD4) counts before ART <200 cells/μl (aHR=2.79, 95%CI: 1.54-5.06), weight-for-age Z score before ART <-2 (aHR=2.38, 95%CI: 1.32-4.26), hemoglobin before ART <80 g/L (aHR=2.47, 95%CI: 1.24-4.92), initial ART with LPV/r (aHR=5.05, 95%CI: 1.15-22.12) were significantly associated with death; being female (aHR=2.23, 95%CI: 1.22-4.07) and initial ART with LPV/r (aHR=2.02, 95%CI: 1.07-3.79) were significantly associated with attrition. Conclusions: The effect of ART in HIV-infected children in Guangxi was better, but the mortality and attrition rates were high within the first year of treatment. It is necessary to strengthen the training in medical staff and health education in HIV-infected children and their parents in order to improve the treatment effect.

[Analysis of HIV transmission hotspots and characteristics of cross-regional transmission in Guangxi Zhuang Autonomous Region based on molecular network]

Objective: To analyze HIV transmission hotspots and characteristics of cross-regional transmission in Guangxi Zhuang autonomous region (Guangxi) based on the molecular network analysis, and provide evidence for optimization of precise AIDS prevention and control strategies. Methods: A total of 5 996 HIV pol sequences sampled from Guangxi between 1997 and 2020 were analyzed together with 165 534 published HIV pol sequences sampled from other regions. HIV-TRACE was used to construct molecular network in a pairwise genetic distance threshold of 0.5%. Results: The proportion of HIV sequences entering the molecular network of HIV transmission hotspots in Guangxi was 31.5% (1 886/5 996). In the molecular network of HIV cross-regional transmission, the links within Guangxi accounted for 51.6% (2 613/5 062), the links between Guangxi and other provinces in China accounted for 48.0% (2 430/5 062), and the links between Guangxi and other countries accounted for 0.4% (19/5 062). The main regions which had cross-regional linked with Guangxi were Guangdong (49.5%, 1 212/2 449), Beijing (17.5%, 430/2 449), Shanghai (6.9%, 168/2 449), Sichuan (5.7%, 140/2 449), Yunnan (4.2%, 102/2 449), Shaanxi (3.8%, 93/2 449), Zhejiang (2.8%, 69/2 449), Hainan (2.0%, 49/2 449), Anhui (1.5%, 37/2 449), Jiangsu (1.3%, 33/2 449), and other regions (each one <1.0%), respectively. The risk factors of entering the molecular network of HIV transmission hotspots in Guangxi included being aged ≥50 years (compared with being aged 25-49 years, aOR=1.68,95%CI:1.46-1.95), males (compared with females, aOR=1.21,95%CI:1.05-1.40), being single (compared with being married, aOR=1.18,95%CI:1.00-1.39), having education level of high school or above (compared with having education level of junior high school or below, aOR=1.21,95%CI:1.04-1.42), acquired HIV through homosexual intercourse (compared with acquired with HIV through heterosexual intercourse, aOR=1.77, 95%CI:1.48-2.12). The risk factors of cross-regional transmission included males (compared with females, aOR=1.74,95%CI:1.13-2.75), having education level of high school or above (compared with having education level of junior high school or below, aOR=1.96,95%CI:1.43-2.69), being freelancer/unemployed/retired (compared with being farmers, aOR=1.50,95%CI:1.07-2.11), acquired HIV through homosexual intercourse (compared with acquired with HIV through heterosexual intercourse, aOR=3.28,95%CI:2.30-4.72). Conclusion: There are HIV transmission hotspots in Guangxi. Guangxi and other provinces in China form a complex cross-regional transmission network. Future studies should carry out social network surveys in high-risk populations inferred from the molecular network analysis for the timely identification of hidden transmission chains and reduction of the second-generation transmission of HIV.

First Measurement of High-Energy Reactor Antineutrinos at Daya Bay

This Letter reports the first measurement of high-energy reactor antineutrinos at Daya Bay, with nearly 9000 inverse beta decay candidates in the prompt energy region of 8-12 MeV observed over 1958 days of data collection. A multivariate analysis is used to separate 2500 signal events from background statistically. The hypothesis of no reactor antineutrinos with neutrino energy above 10 MeV is rejected with a significance of 6.2 standard deviations. A 29% antineutrino flux deficit in the prompt energy region of 8-11 MeV is observed compared to a recent model prediction. We provide the unfolded antineutrino spectrum above 7 MeV as a data-based reference for other experiments. This result provides the first direct observation of the production of antineutrinos from several high-Q_{β} isotopes in commercial reactors.

Efficiently Predicting Vancomycin Resistance of Enterococcus Faecium From MALDI-TOF MS Spectra Using a Deep Learning-Based Approach

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has recently become a useful analytical approach for microbial identification. The presence and absence of specific peaks on MS spectra are commonly used to identify the bacterial species and predict antibiotic-resistant strains. However, the conventional approach using few single peaks would result in insufficient prediction power without using complete information of whole MS spectra. In the past few years, machine learning algorithms have been successfully applied to analyze the MALDI-TOF MS peaks pattern for rapid strain typing. In this study, we developed a convolutional neural network (CNN) method to deal with the complete information of MALDI-TOF MS spectra for detecting Enterococcus faecium, which is one of the leading pathogens in the world. We developed a CNN model to rapidly and accurately predict vancomycin-resistant Enterococcus faecium (VREfm) samples from the whole mass spectra profiles of clinical samples. The CNN models demonstrated good classification performances with the average area under the receiver operating characteristic curve (AUROC) of 0.887 when using external validation data independently. Additionally, we employed the score-class activation mapping (CAM) method to identify the important features of our CNN models and found some discriminative signals that can substantially contribute to detecting the ion of resistance. This study not only utilized the complete information of MALTI-TOF MS data directly but also provided a practical means for rapid detection of VREfm using a deep learning algorithm.

pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature

With the proliferation of genomic sequence data for biomedical research, the exploration of human genetic information by domain experts requires a comprehensive interrogation of large numbers of scientific publications in PubMed. However, a query in PubMed essentially provides search results sorted only by the date of publication. A search engine for retrieving and interpreting complex relations between biomedical concepts in scientific publications remains lacking. Here, we present pubmedKB, a web server designed to extract and visualize semantic relationships between four biomedical entity types: variants, genes, diseases, and chemicals. pubmedKB uses state-of-the-art natural language processing techniques to extract semantic relations from the large number of PubMed abstracts. Currently, over 2 million semantic relations between biomedical entity pairs are extracted from over 33 million PubMed abstracts in pubmedKB. pubmedKB has a user-friendly interface with an interactive semantic graph, enabling the user to easily query entities and explore entity relations. Supporting sentences with the highlighted snippets allow to easily navigate the publications. Combined with a new explorative approach to literature mining and an interactive interface for researchers, pubmedKB thus enables rapid, intelligent searching of the large biomedical literature to provide useful knowledge and insights. pubmedKB is available at https://www.pubmedkb.cc/.

Genome-wide identification of associations between enhancer and alternative splicing in human and mouse

Background

Alternative splicing (AS) increases the diversity of transcriptome and could fine-tune the function of genes, so that understanding the regulation of AS is vital. AS could be regulated by many different cis-regulatory elements, such as enhancer. Enhancer has been experimentally proved to regulate AS in some genes. However, there is a lack of genome-wide studies on the association between enhancer and AS (enhancer-AS association). To bridge the gap, here we developed an integrative analysis on a genome-wide scale to identify enhancer-AS associations in human and mouse.

Result

We collected enhancer datasets which include 28 human and 24 mouse tissues and cell lines, and RNA-seq datasets which are paired with the selected tissues. Combining with data integration and statistical analysis, we identified 3,242 human and 7,716 mouse genes which have significant enhancer-AS associations in at least one tissue. On average, for each gene, about 6% of enhancers in human (5% in mouse) are associated to AS change and for each enhancer, approximately one gene is identified to have enhancer-AS association in both human and mouse. We found that 52% of the human significant (34% in mouse) enhancer-AS associations are the co-existence of homologous genes and homologous enhancers. We further constructed a user-friendly platform, named Visualization of Enhancer-associated Alternative Splicing (VEnAS, http://venas.iis.sinica.edu.tw/), to provide genomic architecture, intuitive association plot, and contingency table of the significant enhancer-AS associations.

Conclusion

This study provides the first genome-wide identification of enhancer-AS associations in human and mouse. The results suggest that a notable portion of enhancers are playing roles in AS regulations. The analyzed results and the proposed platform VEnAS would provide a further understanding of enhancers on regulating alternative splicing.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08537-1.

Joint Determination of Reactor Antineutrino Spectra from ^{235}U and ^{239}Pu Fission by Daya Bay and PROSPECT

A joint determination of the reactor antineutrino spectra resulting from the fission of ^{235}U and ^{239}Pu has been carried out by the Daya Bay and PROSPECT Collaborations. This Letter reports the level of consistency of ^{235}U spectrum measurements from the two experiments and presents new results from a joint analysis of both data sets. The measurements are found to be consistent. The combined analysis reduces the degeneracy between the dominant ^{235}U and ^{239}Pu isotopes and improves the uncertainty of the ^{235}U spectral shape to about 3%. The ^{235}U and ^{239}Pu antineutrino energy spectra are unfolded from the jointly deconvolved reactor spectra using the Wiener-SVD unfolding method, providing a data-based reference for other reactor antineutrino experiments and other applications. This is the first measurement of the ^{235}U and ^{239}Pu spectra based on the combination of experiments at low- and highly enriched uranium reactors.

Ultrasound Localization of Nitinol Wire of Sub-Wavelength Dimension

Goal: To enhance endovascular navigation using surgical guidewires and the use of ionizing radiation, we demonstrate a method for ultrasonic localization of wires with diameters less than the wavelength of ultrasound in the medium. Methods: Nitinol wires with diameters ranging from 50 μm to 250 μm were imaged ultrasonically in a 0.25-in-diameter water-filled tube in a gelatin medium. Imaging frequencies were 5 MHz, 7.5 MHZ, and 10 MHz. Results: For the full range of diameters traversing the phantom, the wires were localized successfully via visual inspection of both regular and difference ultrasound images. Similarly, two convolutional neural networks were trained, and both achieved an accuracy of over 95%. Conclusions: Wires with diameters as small as 50 μm were localized successfully in a water-based gelatin phantom, indicating the potential use of ultrasound to enhance endovascular navigation and surgical treatment.

Termite Pest Identification Method Based on Deep Convolution Neural Networks

Several species of drywood termites, subterranean termites, and fungus-growing termites cause extensive economic losses annually worldwide. Because no universal method is available for controlling all termites, correct species identification is crucial for termite management. Despite deep neural network technologies' promising performance in pest recognition, a method for automatic termite recognition remains lacking. To develop an automated deep learning classifier for termite image recognition suitable for mobile applications, we used smartphones to acquire 18,000 original images each of four termite pest species: Kalotermitidae: Cryptotermes domesticus (Haviland); Rhinotermitidae: Coptotermes formosanus Shiraki and Reticulitermes flaviceps (Oshima); and Termitidae: Odontotermes formosanus (Shiraki). Each original image included multiple individuals, and we applied five image segmentation techniques for capturing individual termites. We used 24,000 individual-termite images (4 species × 2 castes × 3 groups × 1,000 images) for model development and testing. We implemented a termite classification system by using a deep learning-based model, MobileNetV2. Our models achieved high accuracy scores of 0.947, 0.946, and 0.929 for identifying soldiers, workers, and both castes, respectively, which is not significantly different from human expert performance. We further applied image augmentation techniques, including geometrical transformations and intensity transformations, to individual-termite images. The results revealed that the same classification accuracy can be achieved by using 1,000 augmented images derived from only 200 individual-termite images, thus facilitating further model development on the basis of many fewer original images. Our image-based identification system can enable the selection of termite control tools for pest management professionals or homeowners.

NK cell receptor and ligand composition influences the clearance of SARS-CoV-2

To explore how the immune system controls clearance of SARS-CoV-2, we used a single-cell, mass cytometry-based proteomics platform to profile the immune systems of 21 patients who had recovered from SARS-CoV-2 infection without need for admission to an intensive care unit or for mechanical ventilation. We focused on receptors involved in interactions between immune cells and virus-infected cells. We found that the diversity of receptor repertoires on natural killer (NK) cells was negatively correlated with the viral clearance rate. In addition, NK subsets expressing the receptor DNAM1 were increased in patients who more rapidly recovered from infection. Ex vivo functional studies revealed that NK subpopulations with high DNAM1 expression had cytolytic activities in response to target cell stimulation. We also found that SARS-CoV-2 infection induced the expression of CD155 and nectin-4, ligands of DNAM1 and its paired coinhibitory receptor TIGIT, which counterbalanced the cytolytic activities of NK cells. Collectively, our results link the cytolytic immune responses of NK cells to the clearance of SARS-CoV-2 and show that the DNAM1 pathway modulates host-pathogen interactions during SARS-CoV-2 infection.

iTARGEX analysis of yeast deletome reveals novel regulators of transcriptional buffering in S phase and protein turnover

Integrating omics data with quantification of biological traits provides unparalleled opportunities for discovery of genetic regulators by in silico inference. However, current approaches to analyze genetic-perturbation screens are limited by their reliance on annotation libraries for prioritization of hits and subsequent targeted experimentation. Here, we present iTARGEX (identification of Trait-Associated Regulatory Genes via mixture regression using EXpectation maximization), an association framework with no requirement of a priori knowledge of gene function. After creating this tool, we used it to test associations between gene expression profiles and two biological traits in single-gene deletion budding yeast mutants, including transcription homeostasis during S phase and global protein turnover. For each trait, we discovered novel regulators without prior functional annotations. The functional effects of the novel candidates were then validated experimentally, providing solid evidence for their roles in the respective traits. Hence, we conclude that iTARGEX can reliably identify novel factors involved in given biological traits. As such, it is capable of converting genome-wide observations into causal gene function predictions. Further application of iTARGEX in other contexts is expected to facilitate the discovery of new regulators and provide observations for novel mechanistic hypotheses regarding different biological traits and phenotypes.

[Choices of emergency treatment and surgical method for ruptured abdominal aortic aneurysms]

Objective: To investigate the emergency management process of ruptured abdominal aortic aneurysm (RAAA), and analyze the perioperative mortality factors of different surgical methods. Methods: The emergency data and hospitalization data of 91 patients with ruptured abdominal aortic aneurysm in Xiangya Hospital of Central South University from June 2010 to June 2019 were retrospectively analyzed.Twelve of the patients died preoperatively due to excessive blood loss, and the remaining 79 patients were hospitalized for open surgery (OSR) or endovascular repair (EVAR).The differences in age, time to hospital arrival, emergency preparation time, first creatinine value, emergency infusion volume, preoperative drop in blood pressure, preoperative use of vasoactive drugs and iliac artery involvement were compared between preoperative death group (n=12) and preoperative survival group (n=79), OSR group (n=50) and EVAR group (n=29), postoperative death group (n=23) and postoperative survival group (n=56). Results: Seventy-nine patients received open surgery or endovascular repair, and 23 died after operation. Age, time to hospital arrival, first creatinine value and emergency infusion volume were (77±11) years, (18±5)h, (469±150) μmol/L, (4 140±1 743) ml in the preoperative death group and (70±10) years, (12±8) h, (228±174) μmol/L, (1 358±1 211) ml in the preoperative survival group, respectively, and the differences were statistically significant (all P<0.05). There were no significant differences in preoperative data, intraoperative treatment and postoperative perioperative mortality between the open surgery group and the endovascular repair group (all P>0.05). The intraoperative blood loss, operation time and aortic occlusion rate in the endovascular repair group were 100 (50, 175) ml, (3.2±0.9) h, 13.8%, respectively, which were better than that in the open surgery group 1700 (600, 3425) ml, (5.2±1.1) h, 100%. The differences were statistically significant (all P<0.05). Age, emergency preparation time, first creatinine value, emergency infusion volume, blood pressure decline rate and vasoactive drug utilization rate in the death group were (77±8) years, (4.1±1.7) h, (456±172) μmol/L, (2 024±1 687) ml, 100%, 100%, respectively, and (68±10) years, (2.7±2.2) h, (135±26) μmol/L, (1 085±825) ml, 21.4%, 12.5% in the survival group, respectively. The differences were statistically significant (all P<0.05). Conclusions: Age, emergency preparation time, first creatinine value, emergency infusion volume, decreased blood pressure and use of vasoactive drugs are all associated with perioperative death in patients with ruptured abdominal aortic aneurysm. EVAR surgery is a better choice if conditions exist.

[Comparison of the accuracy of intraocular lens power calculation formulas based on the new swept-source optical coherence tomography biometry]

Objective: To compare the accuracy of 6 intraocular lens power calculation formulas based on the new swept-source optical coherence tomography biometry and to analyze the prediction error. Methods: Retrospective case series study. Clinical data were collected from 599 patients (599 eyes) who had underwent uncomplicated phacoemulsification and the IOLMaster 700 examination at the Eye Hospital of Wenzhou Medical University between November 2018 and November 2019. Among the patients, there were 208 males and 391 females with an age of (69±10) years. According to the axial length (AL), eyes were divided into the short AL group (≤22.5 mm, n=100), the normal AL group (>22.5 mm and<25.5 mm, n=375); and the long AL group (≥25.5 mm, n=124). Eyes were also grouped based on the mean keratometry (Km) as flat (≤42.00 D, n=47), normal (>42.00 D to<46.00 D, n=461), and steep (≥46.00 D, n=91), and by anterior chamber depth (ACD) as shallow (≤2.5 mm, n=71), normal (>2.5 mm to<3.5 mm, n=436), and deep (≥3.5 mm, n=92). The median absolute errors (MedAEs) of the Barrett Universal Ⅱ, Haigis, Hoffer Q, Holladay Ⅰ, Holladay Ⅱ, and SRK/T formulas in different AL, Km, and ACD groups were compared using the Friedman test. Results: The differences in MedAE among the 6 formulas of 599 patients (599 eyes) were statistically significant (χ²=120.549, P<0.001). The MedAE of the Barrett Universal Ⅱ formula was smallest (0.35 D), followed by the SRK/T formula (0.36 D). There was no significant difference between the MedAEs of the Barrett universal Ⅱ and Haigis, SRK/T formula (all P=1.000), but there were statistically significant differences among the other formulas (all P<0.01). In different AL groups, the MedAE of each formula was statistically different (χ²=38.307, 38.779, 112.997; all P<0.01).The Barrett Universal Ⅱ formula resulted in the lowest MedAE in the short AL group (0.40 D) and the long AL group (0.31 D). The MedAE of the SRK/T in the normal AL group was lowest (0.35 D). The 6 formulas showed significant differences in MedAE values in different Km groups (χ²=12.284, 90.924, 39.387; all P<0.05).The Haigis formula achieved the lowest MedAE in the flat Km group (0.26 D) and the steep Km group (0.34 D). The Barrett UniversalⅡ formula achieved the lowest MedAE in the normal Km group (0.33 D). The differences in MedAE values of the 6 formulas in different ACD groups were statistically significant (χ²=37.389, 57.643, 52.845; all P<0.01), and the MedAE values of the Barrett Universal Ⅱ in different ACD groups were smallest (0.46, 0.33, 0.31 D). Conclusions: The Barrett Universal Ⅱ formula perform the best over the entire AL range, followed by the Haigis and SRK/T formulas. The Barrett Universal Ⅱ formula result in the lowest prediction error in the short AL group, the long AL group, and all ACD groups. The Haigis formula may be more accurate when the Km was ≤42.00 D or ≥46.00 D. (Chin J Ophthalmol, 2021, 57: 502-511).

[Expression and significance of chemokine CXCL12 and receptor CXCR4 in adenomyosis]

Objective: To observe the expression, correlation and significance of chemokine (C-X-C motif) ligand 12 (CXCL12) and chemokine (C-X-C motif) receptor 4 (CXCR4) in endometrium and myometrium of adenomyosis. Methods: Totally 38 patients were selected in this study, who underwent hysterectomy for adenomyosis at Beijing Obstetrics and Gynecology Hospital from October 2017 to December 2018 as the adenomyosis group, and, in the same period, selected 31 patients with cervical intraepithelial neoplasia Ⅲ or cervical cancer undergoing hysterectomy served as control group. The expression levels of mRNA and protein for CXCL12, CXCR4 in the endometrium and myometrium of the two groups were detected by immunohistochemistry and real-time PCR. Results: (1) The protein levels of CXCL12 and CXCR4 in endometrium in uterus with adenomyosis (0.229±0.025 and 0.226±0.016) were significantly higher than those in endometrium in uterus without adenomyosis (0.153±0.018 and 0.178±0.026); compared with each other, the differences were statistically significant (all P<0.05). And the expressions of CXCL12 and CXCR4 proteins in uterine myometrium of adenomyosis were 0.222±0.045 and 0.126±0.058, respectively, which were higher than those in the control group (0.091±0.029 and 0.099±0.020); compared with each other, the differences were statistically significant (all P<0.05). (2) The expression levels of CXCL12 and CXCR4 mRNA in endometrium of patients with adenomyosis were 6.31±0.12 and 8.49±0.21, respectively, which were higher than those in the control group (1.23±0.10 and 1.36±0.13); compared with each other, the differences were statistically significant (all P<0.05). Moreover, the expression levels of CXCL12 and CXCR4 mRNA in myometrium of patients with adenomyosis were 9.11±0.12 and 8.45±0.16, respectively, which were higher than those in the control group (1.18±0.08 and 1.46±0.13); compared with each other, the differences were statistically significant (all P<0.05). (3) In endometrium and myometrium of uterus with adenomyosis, CXCL12 and CXCR4 mRNA expression levels were positively associated (r=0.478, 0.542, all P<0.05). Conclusions: The levels of CXCL12 and CXCR4 in the endometrium and myometrium of adenomyosis are increased and positively correlated. The two chemokine may be involved in the development of adenomyosis.

Biological Characteristics and Genetic Diversity of Phomopsis asparagi, Causal Agent of Asparagus Stem Blight

Asparagus stem blight is a regional disease. In the present study, we compared strains of Phomopsis asparagi from six different provinces to determine their biological characteristics and genetic diversity, differences in the pycnidium and conidium production, pathogenicity, and growth rate. Considerable differences were established in the pycnidium and conidium production among the P. asparagi strains from the six studied provinces. The largest pycnidium and conidium production had the strains from Fujian, followed by those from Hainan. The virulence of P. asparagi strains was significantly different but without a correlation with the geographical source of the strain. FJ2 had the highest virulence, followed by HN2, SD4, and SD5, whereas SD5 had the lowest virulence. The colony diameter and dry weight of the strains of asparagus stem blight fungus from the six provinces were substantially different. The colonies of HN1-5 had the largest diameters, whereas those of XT1-5, LT1-3, FJ1-5, and SX6 had smaller diameters. Four primers with good repeatability and strong specificity were selected from 100 intersimple sequence repeat (ISSR) primers. ISSR-PCR amplification was performed on 36 strains of asparagus stem blight fungus, and a large number of repeatable DNA fingerprints were obtained. Most of the amplified fragments were within 300 to 500 bp. In all, 69 total points, 64 multiple points, and 92.75% polymorphism points were established. The number of ISSR gene sites detected by four primers ranged from 14 to 20, with an average of 16 multiple sites. The copolymerization was divided into three groups: XT1-5, LT1-3, and FJ1-5, which were clustered into the first group; SD1-6, SX1-6, and HB1-6, clustered into the second group; and HN1-5 in the third group. The results of the cluster analysis revealed that the strains of the neighboring provinces had a nearer phylogenetic relationship than that between distant ones. Therefore, the system evolution of P. asparagi is related to the geographical distribution of its strains.

[Pepsin and bile acids detection in saliva for the diagnosis of gastroesophageal reflux disease]

Objective: To identify the value of the detection of pepsin and bile acids in saliva for the diagnosis of gastroesophageal reflux disease(GERD). Methods: From January 2018 to June 2019, 104 GERD patients and 43 healthy people in Guangdong Provincial People's Hospital were recruited. The 104 patients of GERD group were divided into four sub-groups, including esophageal symptoms GERD group, extraesophageal symptoms GERD group, anxiety or depression group, non-anxiety and non-depression group. Saliva was collected on waking in morning and 2 h after finishing lunch. The concentration of the total pepsin(TPP) and total bile acids(TBA) from saliva was detected by ELISA method. Receiver operating characteristics analysis was used to identify the sensitivity and specificity of the saliva pepsin and bile acids detection. Results: The concentration of TPP in morning waking samples and postprandial samples in the GERD group was 27.1(9.7,50.3) μg/L and 32.4(14.0,58.7) μg/L, the concentration of TBA in postprandial samples was (18.4±2.3)μmol/L, and these levels were significantly higher than that of the control group [7.0(5.1, 9.1) μg/L, 7.4(5.2, 9.4) μg/L, (12.6±5.0)μmol/L](P<0.01). The concentration of TBA in morning waking samples had no significant difference between these two groups(P>0.05). The concentration of TPP and TBA had no significant difference among the four GERD sub-groups(P>0.05).Pepsin in postprandial saliva samples had moderate diagnostic value for GERD, when the saliva pepsin concentration in postprandial samples was higher than 41.33 μg/L, it had a sensitivity of 82.8% and a specificity of 73.3%. The bile acids in saliva had no significant diagnostic value for GERD. Conclusions: Pepsin detection in saliva has a high level of sensitivity and specificity for diagnosing GERD. However, bile acids in saliva has no significant diagnostic value for GERD.

[Characteristics of newly reported HIV/AIDS cases with non-marital or non-commercial heterosexual transmission in Guangxi Zhuang Autonomous Region, 2015-2018]

Objective: To understand the characteristics and associated factors of newly reported HIV/AIDS cases with non-marital or non-commercial heterosexual transmission, in Guangxi Zhuang Autonomous Region (Guangxi), 2015-2018. Methods: Information of newly reported HIV/AIDS cases aged ≥18 years in Guangxi between 2015 and 2018 was collected from the National Comprehensive HIV/AIDS Information System. Unconditional logistic regression model was used to access those factors that were associated with HIV infections through non-marital or non-commercial heterosexual contact. Results: Between 2015 and 2018, a total number of 35 497 HIV/AIDS cases, aged ≥18 years were newly reported in Guangxi. Among them, 32 648 (92.0%) were infected heterosexually while 10 500 were infected through non-marital or non-commercial heterosexual behavior. Non-marital or non-commercial heterosexual transmission accounted for 29.6% (10 500/35 497) of the newly reported HIV/AIDS cases, and 32.2% (10 500/32 648) of those with heterosexual transmission. Males counted for 53.5% (5 617/10 500) of non-marital or non-commercial heterosexual transmission and males to females ratio was 1.2∶1 (5 617∶4 883). Those married or had regular sexual partners counted for 55.9% (5 873/10 500). Commercial heterosexual transmission appeared the main mode of HIV transmission for males (64.4%,16 516/25 633) while main mode for females was non-marital or non-commercial heterosexual transmission and counted for 49.5% (4 883/9 864). Results from the multivariate logistic regression analysis showed that adjusted OR of female HIV/AIDS infected HIV via non-marital or non-commercial heterosexual transmission, was 3.98 times (95%CI: 3.78-4.20) hight than that of males. Among the group aged<50 years and the aged 50-59 years, the adjusted ORs were 1.35 times (95%CI: 1.27-1.44) and 1.13 times (95%CI: 1.05-1.21) hight than that of aged ≥60 years. Those who were single/divorced/widowed, the adjusted OR was 1.53 times (95%CI: 1.45-1.61) hight than that of those married/regular partners. Those with junior high school education, high school education and above the adjusted ORs were 1.22 times (95%CI: 1.16-1.29) and 1.18 times (95%CI: 1.10-1.27), compared to those only with education levels of primary school or below. Conclusions: The number of HIV/AIDS cases via non-marital or non-commercial heterosexual transmission accounted for nearly 30.0% of all the routes of HIV transmission in Guangxi, 2015-2018. Female, aged<60 years old, single/divorced/widowed and having had junior and above high school education etc., appeared as risk factors on non-marital or non-commercial heterosexual transmission, among newly reported HIV/AIDS in Guangxi.

Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach

Eukaryotic transcription factors (TFs) coordinate different upstream signals to regulate the expression of their target genes. To unveil this regulatory network in B-cell receptor signaling, we developed a computational pipeline to systematically analyze the extracellular signal-regulated kinase (ERK)- and IκB kinase (IKK)-dependent transcriptome responses. We combined a bilinear regression method and kinetic modeling to identify the signal-to-TF and TF-to-gene dynamics, respectively. We input a set of time-course experimental data for B cells and concentrated on transcriptional activators. The results show that the combination of TFs differentially controlled by ERK and IKK could contribute divergent expression dynamics in orchestrating the B-cell response. Our findings provide insights into the regulatory mechanisms underlying signal-dependent gene expression in eukaryotic cells.

[Post-marketing multi-center safety surveillance of inactivated enterovirus A71 vaccine (Vero cell)]

Objective: To evaluate the post-marketing safety profiles of the inactivated enterovirus type 71 (EV-A71) vaccine (Vero cell) after routine inoculation. Methods: Eleven cities of Zhejiang Province, Fengtai district of Beijing, Qinnan district, two counties as Pingle and Pingguo of Guangxi Zhuang Autonomous Region, and Dongtai city of Jiangsu Province were selected as the field sites. A total of 45 239 subjects were enrolled in this study from children who seeked the vaccination of EV-A71 vaccine during the period from July, 2016 to June, 2018. Different sampling method were adopted in different sites. All vaccinated children were invited to participate in the study in Fengtai and Dongtai, however, systematic sampling method were adopted in other sites. Active surveillance was conducted and information about adverse reactions (ARs) occurred in 30 min, 3 d and 30 d following each dose of EV-A71 immunization was collected by field observation, phone-call or face-to-face interview. The incidence of ARs in different types, symptoms and grades were described. Results: In total, there were 45 239 children who received 71 243 doses EV-A71 vaccine. The overall incidence of ARs was 1.079% (769 doses), with the highest incidence of 1.182% (177/14 973) in 5-11 month group and the lowest incidence of 0.849% (18/2 119) in ≥ 36 month group among different age groups. There was a higher incidence in solicited ARs, which was 1.047% (746 doses). The incidences of grade 1 and grade 2 ARs were also higher, which were 0.404% (288 doses) and 0.554% (395 doses), respectively. No grade 4 ARs occurred. The doses of the first and the second vaccination was 40 736 and 30 507, respectively, and the incidences of ARs were 1.281% (522 doses) and 0.810% (247 doses). Also, the incidences of ARs were 0.091% (37 doses) and 0.043% (13 doses) in local, and 1.168% (476 doses) and 0.760% (232 doses) in system. The symptoms of ARs after the two doses of vaccination were basically the same. Redness at the injection site was the most common local ARs after each dose vaccination, with doses of 24 and 11, while fever was the most common systemic ARs, with doses of 362 and 190. Moreover, ARs mainly occurred in 30 min to 3 d after each dose vaccination, with incidence of 1.016% (414 doses) and 0.698% (213 doses) in the first and second dose, respectively. Conclusion: The ARs had a low incidence after vaccination in children and most were mild or moderate. EV-A71 vaccine with good safety is suitable for inoculation in a large scale.

CATANA: a tool for generating comprehensive annotations of alternative transcript events

SUMMARY

In higher eukaryotes, the generation of transcript isoforms from a single gene through alternative splicing (AS) and alternative transcription (AT) mechanisms increases functional and regulatory diversities. Annotating these alternative transcript events is essential for genomic studies. However, there are no existing tools that generate comprehensive annotations of all these alternative transcript events including both AS and AT events. In the present study, we develop CATANA, with the encoded exon usage patterns based on the flattened gene model, to identify ten types of AS and AT events. We demonstrate the power and versatility of CATANA by showing greater depth of annotations of alternative transcript events according to either genome annotation or RNA-seq data.

AVAILABILITY AND IMPLEMENTATION

CATANA is available on https://github.com/shiauck/CATANA.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Borders of Cis-Regulatory DNA Sequences Preferentially Harbor the Divergent Transcription Factor Binding Motifs in the Human Genome

Changes in cis-regulatory DNA sequences and transcription factor (TF) repertoires provide major sources of phenotypic diversity that shape the evolution of gene regulation in eukaryotes. The DNA-binding specificities of TFs may be diversified or produce new variants in different eukaryotic species. However, it is currently unclear how various levels of divergence in TF DNA-binding specificities or motifs became introduced into the cis-regulatory DNA regions of the genome over evolutionary time. Here, we first estimated the evolutionary divergence levels of TF binding motifs and quantified their occurrence at DNase I-hypersensitive sites. Results from our in silico motif scan and experimentally derived chromatin immunoprecipitation (TF-ChIP) show that the divergent motifs tend to be introduced in the edges of cis-regulatory regions, which is probably accompanied by the expansion of the accessible core of promoter-associated regulatory elements during evolution. We also find that the genes neighboring the expanded cis-regulatory regions with the most divergent motifs are associated with functions like development and morphogenesis. Accordingly, we propose that the accumulation of divergent motifs in the edges of cis-regulatory regions provides a functional mechanism for the evolution of divergent regulatory circuits.

[Dynamic variations of BMI and influencing factors among HIV/AIDS patients receiving highly active antiretroviral therapy in Liuzhou, Guangxi Zhuang Autonomous Region, 2013-2014]

Objective: To understand the dynamic variation of BMI and influencing factors among HIV/AIDS patients receiving highly active anti-retroviral therapy (HAART) in Liuzhou, Guangxi Zhuang Autonomous Region (Guangxi). Methods: HIV/AIDS patients receiving HAART for the first time since 1 January 2013 were selected. Data on BMI was analyzed among patients receiving HAART at baseline,6 months and 12 months after treatment. By using the general linear model repeated measures of analysis of variance, BMI dynamic variations and influencing factors were described and analyzed. Results: The average BMI of 2 871 patients at baseline, 6th months and 12th months appeared as (20.65±3.32), (20.87±3.22) and (21.18±3.20), respectively, with differences all statistically significant (F=18.86, P<0.001). BMI were increasing over time with treatments (F=37.25, P<0.001). Main influencing factors were noticed as: age, sex, marital status, baseline data of CD(4)(+)T cells and the WHO classification on clinical stages. Conclusions: Higher proportion of BMI malnutrition counts was seen among patients before receiving HAART in Liuzhou. BMI of the patients that were on HAART seemed being influenced by many factors. It is necessary to select appropriate treatment protocols on different patients so as to improve the nutritional status of the patients.

Practical Use of RNA Interference: Oral Delivery of Double-stranded RNA in Liposome Carriers for Cockroaches

RNA interference (RNAi) has been widely applied for uncovering the biological functions of numerous genes, and has been envisaged as a pest control tool operating by disruption of essential gene expression. Although different methods, such as injection, feeding, and soaking, have been reported for successful delivery of double-stranded RNA (dsRNA), the efficiency of RNAi through oral delivery of dsRNA is highly variable among different insect groups. The German cockroach, Blattella germanica, is highly sensitive to the injection of dsRNA, as shown by many studies published previously. The present study describes a method to demonstrate that the dsRNA encapsulated with liposome carriers is sufficient to retard the degradation of dsRNA by midgut juice. Notably, the continuous feeding of dsRNA encapsulated by liposomes significantly reduces the tubulin expression in the midgut, and led to the death of cockroaches. In conclusion, the formulation and utilization of dsRNA lipoplexes, which protect dsRNA against nucleases, could be a practical use of RNAi for insect pest control in the future.

Cellular and molecular remodelling of a host cell for vertical transmission of bacterial symbionts

Various insects require intracellular bacteria that are restricted to specialized cells (bacteriocytes) and are transmitted vertically via the female ovary, but the transmission mechanisms are obscure. We hypothesized that, in the whitefly Bemisia tabaci, where intact bacteriocytes (and not isolated bacteria) are transferred to oocytes, the transmission mechanism would be evident as cellular and molecular differences between the nymph (pre-adult) and adult bacteriocytes. We demonstrate dramatic remodelling of bacteriocytes at the developmental transition from nymph to adulthood. This transition involves the loss of cell-cell adhesion, high division rates to constant cell size and onset of cell mobility, enabling the bacteriocytes to crawl to the ovaries. These changes are accompanied by cytoskeleton reorganization and changes in gene expression: genes functioning in cell-cell adhesion display reduced expression and genes involved in cell division, cell motility and endocytosis/exocytosis have elevated expression in adult bacteriocytes, relative to nymph bacteriocytes. This study demonstrates, for the first time, how developmentally orchestrated remodelling of gene expression and correlated changes in cell behaviour underpin the capacity of bacteriocytes to mediate the vertical transmission and persistence of the symbiotic bacteria on which the insect host depends.

Oral delivery of dsRNA lipoplexes to German cockroach protects dsRNA from degradation and induces RNAi response

BACKGROUND

In the past years, the concept of RNAi application for insect pest control has been proposed, considering the disruption of vital genes. However, the efficiency of RNAi is variable between different insect groups, especially by oral delivery of dsRNA. The purpose of this study is to assess the possibilities of RNAi as a tool for pest control using oral delivery of the dsRNAs encapsulated by liposome in the German cockroach Blattella germanica, which is highly sensitive to RNAi by injection of dsRNAs.

RESULTS

Injecting dsRNA into the abdomen of B. germanica caused dramatic depletion of essential α-tubulin gene and mortality. In contrast, oral delivery of the naked dsRNA resulted in lower RNAi efficiency, accounting for rapid degradation of the dsRNA in the midgut of B. germanica. Notably, we have further demonstrated that continuous ingestion of dsRNA lipoplexes in which dsRNA was encapsulated with a cationic liposome carrier was sufficient to slow down the degradation of dsRNA in the midgut and to increase the mortality of the German cockroach by significantly inhibiting α-tubulin expression in the midgut.

CONCLUSION

We provide empirical evidence that the formulation of dsRNA lipoplexes could be a plausible approach for insect pest control based on RNAi. © 2016 Society of Chemical Industry.

IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes

Database URL

http://isoplot.iis.sinica.edu.tw/.

Application of 3D printing technology on the treatment of complex proximal humeral fractures (Neer3-part and 4-part) in old people

PURPOSE

This study was conducted to investigate the feasibility and clinical potential of using the 3D printing technology (3DPT) versus typical strategy (thin-layer CT scan) for the treatment of complicated proximal humeral fractures (PHFs) in old people.

METHODS

Sixty-six old patients age ranging from 61 to 76 years with persistent complicated PHFs were randomly assigned to two groups as per the controlled randomization table (34 cases in the test group and 32 cases in the control group). In the test group, 3DPT was applied to build the 3D facture model of a patient, according to the data acquired from the thin-layer CT scan and subsequently processed with Mimics software. This helped to confirm the diagnosis, design the individual operation plan, simulate the surgical procedures and perform the surgery as plan. In the control group, only thin-layer CT scan was applied for the design of the operation plan prior to the surgery. Here, parameters including surgery duration, blood loss volume during surgery, the number of fluoroscopy, time to union were statistically analyzed for two groups after the operation. The screw lengths designed before the surgery and measured during the surgery were compared.

RESULTS

The 3D PHF model generated using 3DPT was able to provide the visual display and omni-directional observation of the direction and severity of the fracture dislocation, which facilitated preoperative diagnosis, operation planning and design, data measurement, preselection of internal fixator and surgical outcome simulation. According to the follow-up ranging from 12∼28 months for the 66 patients, the results showed no significant difference in time to union between the two groups (P>0.05). Apart from that, less surgery duration, less blood loss during surgery, less number of fluoroscopy can be observed compared with the control group (P<0.05).

CONCLUSIONS

In this study, 3DPT showed great clinical feasibility of the treatment of complicated PHFs. The 3D-print PHF model had the ability to clearly display the fracture and thus was useful to determine the fracture classification and the magnitude of fracture injury. It benefited surgeons to gain a better understanding of complicated PHFs, design a most suitable operation plan prior to surgery and facilitate the doctor-patient communication. This therefore enabled the reduction of intraoperative injury and the optimization of surgical outcomes.

[Clinical application of multi-electrode synchronous radiofrequency ablation via switching controller for treating large hepatocellular carcinoma]

Objective: To explore the preliminary clinical efficacy and safety of multi-electrode synchronous radiofrequency ablation via switching controller for treating large hepatocellular carcinoma. Methods: A total of 20 patients with large hepatocellular carcinoma from minimally invasive Interventional department of Sun Yat-sen University Cancer Center were enrolled in this retrospective study from December 2013 to December 2014.The procedures were conducted with multi-electrode synchronous radiofrequency ablation via switching controller under CT guidance.The necrosis rate of tumor was assessed by the following imaging examination.The single factor analysis of variance (ANOVA) was employed to compare the total bilirubin, albumin, renal function, blood coagulation function before and after ablation, to evaluate the safety of treatment. Result: Twenty patients with a total of 31 lesions accepted 23 times ablation procedures using multi-electrode synchronous radiofrequency ablation via switching controller.The recent evaluation after treatment was as followed: complete necrosis rate 51.6% (16/31), nearly complete necrosis rate 22.6% (7/31), partial necrosis rate 9.7% (3/31), treatment effectiveness rate (necrosis rate > 50%) 83.9%.The necrosis rate which was less than half volume of the tumor was only seen in 5 cases with huge hepatocellular carcinoma (16.1%). No dead cases appeared after ablation procedures.The patients' total bilirubin elevated moderately after ablation procedures and reversed to normal level after liver function protection treatment.There were no statistical differences of renal function and blood coagulation function before and after ablation.After ablation procedures, 5 cases (21.7%, 5/23) appeared fever, 6 cases (26.1%) with vomiting, only 3 cases (13.0%, 3/23) with moderately severe pain in 3 days after ablation and remitted after taking oral analgesics in one week. Conclusion: The clinical efficacy of multi-electrode synchronous radiofrequency ablation via switching controller for large hepatocellular carcinoma is satisfactory with guaranteed security, which can be a choice for treating large hepatocellular carcinoma.

[Finite element analysis of astigmatic keratotomy based on corneal biomechanical properties]

OBJECTIVE

To establish a finite-element biomechanical model of astigmatic keratotomy, and to investigate the impact of surgical parameters on corneal deformation, stress distribution and astigmatism correction.

METHODS

With Rhinoceros modeling and Abaqus finite element analysis software, a three-dimensional finite-element model of astigmatic cornea was developed, and surgical parameters such as incision optical zone, incision depth and length were varied. Postoperative corneal stress, apical deformation and astigmatism correction were assessed.

RESULTS

A significant increase of stress was noticed near corneal incisions, and maximum corneal stress decreased with the increase of incision depth. Both anterior and posterior corneal surface moved slightly forward postoperatively. Maximum corneal stress was 340 392, 361 022 and 214 187 Pa, and anterior and posterior apical deformation was 49.80, 51.64, 55.53 μm and 54.15, 55.91, 59.67 μm, with 45°, 60° and 90° in arc length of the incision, respectively. The refractive power decreased in steep meridian and increased in flat meridian, resulting in a total decrease of corneal astigmatism. The magnitude of astigmatism correction was 0.85, 1.59, 2.23 and 3.06 D with 30°, 45°, 60° and 90° in arc length of the incision, respectively.

CONCLUSIONS

The finite-element biomechanical model of astigmatic keratotomy could be used to predict the optical outcomes after surgery. The magnitude of astigmatism correction is positively correlated with the surgical incision arc length. (Chin J Ophthalmol, 2016, 52: 674-680).

[Phenotypic characteristics of LAP(+) CD4(+) T lymphocytes in colorectal cancer tissues]

OBJECTIVE

To analyze the phenotypic characteristics of LAP(+) CD4(+) T lymphocytes and investigate their molecular mechanisms in colorectal cancer (CRC) microenvironment.

METHODS

Fifty colorectal cancer patients treated in our two hospitals from January 2014 to May 2014 were included in this study. Their tumor tissues and adjacent normal tissues, peripheral blood samples, and peripheral blood samples of 25 healthy donors (HD) were collected to isolate the lymphocytes. The different expressions of CCR7, CD45RA, Foxp3, CTLA-4, CCR4 and CCR5 in LAP(+) CD4(+) T and LAP(-)CD4(+) T lymphocytes were analyzed by flow cytometry (FCM).

RESULTS

The FCM assay detected that the percentage of LAP(+) CD4(+) T cells in peripheral blood of the CRC patients were significantly higher than that of HD [(9.44±3.18)% versus (1.49±1.00)%, P<0.001]. In addition, significantly more LAP(+) CD4(+) T cells were also recruited into tumor tissue than those in the tumor-adjacent normal tissue [(11.76±3.74)% versus (3.87±1.64)%, P<0.001]. LAP(+) CD4(+) T cells in the tumor-adjacent normal tissue and peripheral blood of both HDs and CRC patients mainly displayed a central memory phenotype. However, effector memory lymphocytes were predominant in the tumor tissue.In the tumor tissue, the expression of Foxp3 in the LAP(+) CD4(+) T cells was (3.87±1.12)%, significantly lower than that in the LAP(-)CD4(+) T cells (16.70±2.61)%, (P<0.001); the expression of CTLA-4 in the LAP(+) CD4(+) T cells was (36.36±19.14)%, significantly higher than the (19.60±8.91)% in the LAP(-)CD4(+) T cells (P<0.001); the expression of CCR4 in the LAP(+) CD4(+) T cells was (37.72±11.14)%, significantly higher than the (30.06±9.14)% in the LAP(-)CD4(+) T cells (P<0.001); and the expression of CCR5 in the LAP(+) CD4(+) T cells was (18.86±7.10)%, significantly higher than the (13.92±3.31)% in the LAP(-)CD4(+) T cells (P<0.001).

CONCLUSIONS

LAP(+) CD4(+) T cells with low expression of Foxp3 and high expressions of CTLA-4, CCR4 and CCR5 are tend to be enriched and accumulated in the tumor tissue. The unique phenotypic characteristics make these cells a distinct subset of lymphocytes, apparently different from the traditional CD4(+) CD25(+) Treg cells.

Consumption of dietary sugar by gut bacteria determines Drosophila lipid content

Gut microorganisms are essential for the nutritional health of many animals, but the underlying mechanisms are poorly understood. This study investigated how lipid accumulation by adult Drosophila melanogaster is reduced in flies associated with the bacterium Acetobacter tropicalis which displays oral-faecal cycling between the gut and food. We demonstrate that the lower lipid content of A. tropicalis-colonized flies relative to bacteria-free flies is linked with a parallel bacterial-mediated reduction in food glucose content; and can be accounted for quantitatively by the amount of glucose acquired by the flies, as determined from the feeding rate and assimilation efficiency of bacteria-free and A. tropicalis-colonized flies. We recommend that nutritional studies on Drosophila include empirical quantification of food nutrient content, to account for likely microbial-mediated effects on diet composition. More broadly, this study demonstrates that selective consumption of dietary constituents by microorganisms can alter the nutritional balance of food and, thereby, influence the nutritional status of the animal host.

Pyrroloquinoline quinone enhances the resistance to oxidative stress and extends lifespan upon DAF-16 and SKN-1 activities in C. elegans

Pyrroloquinoline quinone (PQQ) is linked to fundamental biological processes such as mitochondrial biogenesis and lipid metabolism. PQQ may also function as an essential micronutrient during animal development. Recent studies have shown the therapeutic potential of PQQ for several age-related diseases due to its antioxidant capacity. However, whether PQQ can promote longevity is unknown. Here, we investigate the effects of PQQ on oxidative stress resistance as well as lifespan modulation in Caenorhabditis elegans. We find that PQQ enhances resistance to oxidative stress and extends the lifespan of C. elegans at optimal doses. The underlying molecular mechanism involves the increased activities of the primary lifespan extension transcriptional factors DAF-16/FOXO, the conserved oxidative stress-responsive transcription factor SKN-1/Nrf2, and upregulation of daf-16, skn-1 downstream targets including sod-3, hsp16.2, gst-1 and gst-10. Our findings uncover a novel role of PQQ in longevity, supporting PQQ as a possible dietary supplement for overall health improvement.

Note: Enhancing the sensitivity of roll-angle measurement with a novel interferometric configuration based on waveplates and folding mirror

A novel method for very high resolution measurement of roll angle on a transparent plate is developed theoretically and tested experimentally. The new optical configuration is based on the interferometric readout of phase shift accumulated on the double passage through half wave plate, together with a careful control of polarization state by means of quarter wave plate, and optimizing the tilt of the folding mirror. Sensitivity to roll angle is greatly enhanced and a gain coefficient exceeding 700 is found theoretically, based on Jones' matrix analysis, with a 6-fold increase respect to previous results. In the experimental setup, at the optimum 36° incidence to retroreflector, we measured a gain coefficient of 340. Correspondingly, with an interferometer phase meter resolving 0.01°, a roll-angle resolution 0.1-arc sec is attained.

The multi-tasking gut epithelium of insects

The insect gut epithelium plays a vital role in multiple processes, including nutrition, immunity and osmoregulation. Recent research is revealing the molecular and biochemical basis of these functions. For example, the pattern of nutrient acquisition by the gut epithelium is integrated into the overall regulation of nutrient allocation, as illustrated by evidence for systemic controls over expression of key genes coding digestive enzymes and transporters in carbohydrate acquisition; and the abundance and diversity of microorganisms in the gut lumen is regulated by multiple molecular properties of the gut epithelial cells, including the synthesis of enzymes that produce reactive oxygen species and anti-microbial peptides. These traits are underpinned by the function of the gut epithelium as a selective barrier which mediates the controlled movement of water, ions, metabolites and macromolecules between the gut lumen and insect tissues. Breakdown of the gut epithelial barrier has been implicated in muscle paralysis of insects at low temperatures (chill coma) and in aging. The key challenge for future research is to understand how the multiple functions of the insect gut epithelium are integrated by signaling interactions among epithelial cells, the gut microbiota and other insect organs.